The Belgian added the ATP 250 event to the crown he won in Kitzbuhel in August by beating sixth seed Sousa 6-4 6-3 in Metz.
Goffin, the eighth seed, made a strong start to the match by breaking the Portuguese at the first opportunity and went on to take the opener on his sixth set point.
The 23-year-old began the second set strongly as well, breaking Sousa in the very first game to set the tone for the decider.
Goffin did give up two break points in the fourth game of the set, but Sousa failed to take advantage.
The Belgian quickly regained his composure to hold and, from that point on, did not drop a single point on his serve for the remainder of the match.
And he wrapped matters up at the second opportunity to condemn Sousa to his second final defeat of the season after his loss to Pablo Cuevas in Bastad.